A new system was installed to automatically download and index
new Ensembl releases. A new computer with four CPUs, 2Tb winchester capacity
and 8Gb memory was installed. This highly accelerates computing times
and enables us to index new genomes if required.

Feb 04, 2008, Version 2.08 - tusi

A new menu point, "Genome builds" has been added to help to find
information about what version of the genome builds or
database are used by the BiSearch Web Server.

Feb 01, 2008, Version 2.07 - tusi

Preprocessing of the input primer for genome search has been
modified. Previously the input primers were bisulfite treated by
the software before the search on the bisulfite treated genome
if the primers were not designed for the amplification of the
sense strand. This modification step has been removed from the
software.

Jun 16, 2006, Version 2.06 - tusi

Multiple primer pairs can be submitted for ePCR in one file.
Each line in the uploaded file should contain a
primer pair preceeded by an ID. Primer sequences should be separated
by space.

BiSearch Web Server has been redesigned. All codes and pages were
rewritten. The new fpcr algorithm was included in the server. Therefore
no need to store and e-mail genome search results to users. This new
feature led to us to free the server from registration. Academic
users are allowed to use the server free and without registration.
The newly designed server has a lot of new features:

Parameters are stored by the user's web browser, using cookies;

Parameters are grouped for the various tasks, therefore users can
easily find and edit them;

Parameters can be shown for each separate tasks, either for set them
before calculation/searching or after it in the result page;

A new online help system was integrated to the server to help users
to fill in the various input forms;

Result's page of primer design are brushed up by some javascript codes
showing the vaious primer's annealings and PCR products in a tooltip
window, while the mouse is over the result table cells;

After primer design, primer genome search can be done only separately.

The greatest achivement on the server is the integration of FPCR
algorithm into the genome search. FPCR (Fast PCR) algorithm uses
constant 16mer oligonucleotides for searching. The search is done by
applying hash matrices. A typical search is done within one minute
(for comparison: by using the old search algorithm a typical
bisulfite prepared primer genome search was taken about 20 minutes).

Dec 05, 2005, Version 1.99 - tusi

A very fast pcr algorithm was coded. Fixed 16mer oligonucleotid
sequences can be searched in the genome. We need some fast and large winchester
to use this new fpcr algorithm.

Feb 21, 2005, Version 1.0.5 - tusi

BiSearch Web Server has been moved to a new machine, which is 1.5 times faster than previous one.

Jan 22, 2005, Version 1.0.4 - tusi

Commercial users are allowed to use the server in a test mode. That is they are allowed to run the Primer Design on bisulfite treated sample tools five times, and five times the Genome Search tool either with their own primers or with primer designed by the server. Commercial users may allowed to use the other tools on this server unlimitedly.

Commercial users can apply the test LICENSE AGREEMENT by using this link.

A new logo was added to the server.

Dec 14, 2004, Version 1.0.3 - tusi

New feature: default parameter set can be restored by clicking "Get Default Values" on the Set parameters page.

Default value of minimum primer length was increased to 20.

Primer search range is set to 0-n/2 and n/2-n for forward and reverse primer, respectively, where n is the length of the sequence.

New feature: user can select between "specific" and "more specific" primer design parameters in the case of MSP, where "specific" means that only one of the two primers has CpG site it's 3' end, while "more specific" means that both primers have to be CpG site their 3' end.

If more than 10000 hit is found during the primer genome search, only the number of hits is written to the output, rather than enumerating each hits.

Nov 29, 2004, Version 1.0.2 - tusi

User login system changed. Now, users may store they data on the BiSearch Web Server for a week. They can reread their former results file. After finishing genome search BiSearch Web Server send only a notification to the user instead of sending the whole results, which can be some tens megabyte.